|
| Status |
Public on Nov 24, 2020 |
| Title |
Australian AD S57 |
| Sample type |
RNA |
| |
|
| Source name |
prefrontal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prefrontal cortex
diagnosis: Alcohol
age: 50
Sex: Male
rin: 3.6
brain weight: 1420
ph: 6.59
pmi: 24
hemisphere: 0
neuropathology: 1
hepatology: 1
toxicology: 1
smoking: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing the small RNA fraction was isolated from 100mg fresh frozen tissue from the prefrontal cortex (PFC) using the mirVana-PARIS kit (Life Technologies, Carlsbad, CA) following manufacturer's protocols. RNA concentration was measured using the Quant-iT Broad Range RNA Assay kit (Life Technologies) and the RNA Integrity Number (RIN) was measured on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Starting from 300ng of total RNA, cDNA synthesis and cRNA labelling were performed using the GeneChip 3' IVT Express Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Ten µg of fragmented cRNA were hybridized on the Affymetrix GeneChip Human Genome U133A 2.0 (HG-U133A 2.0).
|
| Scan protocol |
Each array was scanned on the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) and raw probe intensities stored in .CEL files by the GeneChip Operating Software (GCOS v1.4).
|
| Data processing |
Array quality was assessed by monitoring the ratios of GAPDH and by the percentage of Present genes (%P) and array exhibiting GAPDH 3 and %P > 40% were considered of good quality. Expression values were calculated following the pre-processing procedure: 1) GCRMA background correction, 2) log2 transformation, 3) quantile normalization and 4) median-polish probeset summarization using Partek Genomics Suite (PGS) v6.23 (PGS; Partek Inc., St. Louis, MO). The batch effect removal option in PGS was used to control for batch effect. mRNA and miRNA microarray quality was further assessed using a principal components analysis (PCA) which was conducted on the expression values for both array types in which samples were plotted along the first three principle components (PCs) to identify potential microarray outliers.
|
| |
|
| Submission date |
Nov 23, 2020 |
| Last update date |
Nov 24, 2020 |
| Contact name |
Eric Vornholt |
| E-mail(s) |
eric.vornholt@mssm.edu
|
| Phone |
15205487115
|
| Organization name |
Icahn School of Medicine
|
| Street address |
800 E. Leigh St. Box 980126
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE161986 |
Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in the NAc and PFC [mRNA] |
| GSE161999 |
Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in the NAc and PFC |
|
